Maize protein structure resources at the maize genetics and genomics database.

Protein structures play an important role in bioinformatics, such as in predicting gene function or validating gene model annotation. However, determining protein structure was, until now, costly and time-consuming, which resulted in a structural biology bottleneck. With the release of such programs AlphaFold and ESMFold, this bottleneck has been reduced by several orders of magnitude, permitting protein structural comparisons of entire genomes within reasonable timeframes. MaizeGDB has leveraged this technological breakthrough by offering several new tools to accelerate protein structural comparisons between maize and other plants as well as human and yeast outgroups. MaizeGDB also offers bulk downloads of these comparative protein structure data, along with predicted functional annotation information. In this way, MaizeGDB is poised to assist maize researchers in assessing functional homology, gene model annotation quality, and other information unavailable to maize scientists even a few years ago.

A pan-genomic approach to genome databases using maize as a model system.

Research in the past decade has demonstrated that a single reference genome is not representative of a species' diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.

MaizeDIG: Maize Database of Images and Genomes.

Background: An organism can be described by its observable features (phenotypes) and the genes and genomic information (genotypes) that cause these phenotypes. For many decades, researchers have tried to find relationships between genotypes and phenotypes, and great strides have been made. However, improved methods and tools for discovering and visualizing these phenotypic relationships are still needed. The maize genetics and genomics database (MaizeGDB, www.maizegdb.org) provides an array of useful resources for diverse data types including thousands of images related to mutant phenotypes in Zea mays ssp. mays (maize). To integrate mutant phenotype images with genomics information, we implemented and enhanced the web-based software package BioDIG (Biological Database of Images and Genomes). Findings: We developed a genotype-phenotype database for maize called MaizeDIG. MaizeDIG has several enhancements over the original BioDIG package. MaizeDIG, which supports multiple reference genome assemblies, is seamlessly integrated with genome browsers to accommodate custom tracks showing tagged mutant phenotypes images in their genomic context and allows for custom tagging of images to highlight the phenotype. This is accomplished through an updated interface allowing users to create image-to-gene links and is accessible via the image search tool. Conclusions: We have created a user-friendly and extensible web-based resource called MaizeDIG. MaizeDIG is preloaded with 2,396 images that are available on genome browsers for 10 different maize reference genomes. Approximately 90 images of classically defined maize genes have been manually annotated. MaizeDIG is available at http://maizedig.maizegdb.org/. The code is free and open source and can be found at https://github.com/Maize-Genetics-and-Genomics-Database/maizedig.

MaizeGDB 2018: the maize multi-genome genetics and genomics database.

Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly. Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding. MaizeGDB hosts a wide range of data including recent support of new data types including genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data (SNPversity), download and compare gene expression data (qTeller), visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user-specified queries to the MaizeGDB database (MaizeMine). MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible. MaizeGDB is accessible online at https://www.maizegdb.org.

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation.

The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders' needs for visualizing pedigrees, diversity data and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on behalf of the Maize Genetics Executive Committee in Summer 2015. The survey garnered 48 responses from maize researchers, of which more than half were self-identified as breeders. The survey showed that the maize researchers considered their top priorities for visualization as: (i) displaying single nucleotide polymorphisms in a given region for a given list of lines, (ii) showing haplotypes for a given list of lines and (iii) presenting pedigree relationships visually. The survey also asked which populations would be most useful to display. The following two populations were on top of the list: (i) 3000 publicly available maize inbred lines used in Romay et al. (Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol, 2013;14:R55) and (ii) maize lines with expired Plant Variety Protection Act (ex-PVP) certificates. Driven by this strong stakeholder input, MaizeGDB staff are currently working in four areas to improve its interface and web-based tools: (i) presenting immediate progenies of currently available stocks at the MaizeGDB Stock pages, (ii) displaying the most recent ex-PVP lines described in the Germplasm Resources Information Network (GRIN) on the MaizeGDB Stock pages, (iii) developing network views of pedigree relationships and (iv) visualizing genotypes from SNP-based diversity datasets. These survey results can help other biological databases to direct their efforts according to user preferences as they serve similar types of data sets for their communities. Database URL: https://www.maizegdb.org.

MaizeGDB update: new tools, data and interface for the maize model organism database.

MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, the original maize genetics database MaizeDB was created. In 2003, the combined contents of MaizeDB and the sequence data from ZmDB were made accessible as a single resource named MaizeGDB. Over the next decade, MaizeGDB became more sequence driven while still maintaining traditional maize genetics datasets. This enabled the project to meet the continued growing and evolving needs of the maize research community, yet the interface and underlying infrastructure remained unchanged. In 2015, the MaizeGDB team completed a multi-year effort to update the MaizeGDB resource by reorganizing existing data, upgrading hardware and infrastructure, creating new tools, incorporating new data types (including diversity data, expression data, gene models, and metabolic pathways), and developing and deploying a modern interface. In addition to coordinating a data resource, the MaizeGDB team coordinates activities and provides technical support to the maize research community. MaizeGDB is accessible online at http://www.maizegdb.org.

MaizeGDB: curation and outreach go hand-in-hand.

First released in 1991 with the name MaizeDB, the Maize Genetics and Genomics Database, now MaizeGDB, celebrates its 20th anniversary this year. MaizeGDB has transitioned from a focus on comprehensive curation of the literature, genetic maps and stocks to a paradigm that accommodates the recent release of a reference maize genome sequence, multiple diverse maize genomes and sequence-based gene expression data sets. The MaizeGDB Team is relatively small, and relies heavily on the research community to provide data, nomenclature standards and most importantly, to recommend future directions, priorities and strategies. Key aspects of MaizeGDB's intimate interaction with the community are the co-location of curators with maize research groups in multiple locations across the USA as well as coordination with MaizeGDB's close partner, the Maize Genetics Cooperation--Stock Center. In this report, we describe how the MaizeGDB Team currently interacts with the maize research community and our plan for future interactions that will support updates to the functional and structural annotation of the B73 reference genome.

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is 'Using the MaizeGDB Genome Browser', which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser. Database

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.

The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time-sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn's utility are provided herein.

Choosing a genome browser for a Model Organism Database: surveying the maize community.

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers' needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers' needs. Here, we document the survey's outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/

The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps.

SUMMARY: Methods to automatically integrate sequence information with physical and genetic maps are scarce. The Locus Lookup tool enables researchers to define windows of genomic sequence likely to contain loci of interest where only genetic or physical mapping associations are reported. Using the Locus Lookup tool, researchers will be able to locate specific genes more efficiently that will ultimately help them develop a better maize plant. With the availability of the well-documented source code, the tool can be easily adapted to other biological systems. AVAILABILITY: The Locus Lookup tool is available on the web at http://maizegdb.org/cgi-bin/locus_lookup.cgi. It is implemented in PHP, Oracle and Apache, with all major browsers supported. Source code is freely available for download at http://ftp.maizegdb.org/open_source/locus_lookup/.

MaizeGDB becomes 'sequence-centric'.

MaizeGDB is the maize research community's central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays. The MaizeGDB team endeavors to meet research needs as they evolve based on researcher feedback and guidance. Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluqueño genomes. Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects' data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation. In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users. MaizeGDB is accessible online at http://www.maizegdb.org.Database URL:http://www.maizegdb.org.

MaizeGDB: The maize model organism database for basic, translational, and applied research.

In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, the outcomes of which drive breeding and product development. In order for basic, translational, and applied researchers to benefit from others' investigations, newly generated data must be made freely and easily accessible. MaizeGDB is the maize research community's central repository for genetics and genomics information. The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities.

Functional analysis of maize RAD51 in meiosis and double-strand break repair.

In Saccharomyces cerevisiae, Rad51p plays a central role in homologous recombination and the repair of double-strand breaks (DSBs). Double mutants of the two Zea mays L. (maize) rad51 homologs are viable and develop well under normal conditions, but are male sterile and have substantially reduced seed set. Light microscopic analyses of male meiosis in these plants reveal reduced homologous pairing, synapsis of nonhomologous chromosomes, reduced bivalents at diakinesis, numerous chromosome breaks at anaphase I, and that >33% of quartets carry cells that either lack an organized nucleolus or have two nucleoli. This indicates that RAD51 is required for efficient chromosome pairing and its absence results in nonhomologous pairing and synapsis. These phenotypes differ from those of an Arabidopsis rad51 mutant that exhibits completely disrupted chromosome pairing and synapsis during meiosis. Unexpectedly, surviving female gametes produced by maize rad51 double mutants are euploid and exhibit near-normal rates of meiotic crossovers. The finding that maize rad51 double mutant embryos are extremely susceptible to radiation-induced DSBs demonstrates a conserved role for RAD51 in the repair of mitotic DSBs in plants, vertebrates, and yeast.

MaizeGDB's new data types, resources and activities.

MaizeGDB is the Maize Genetics and Genomics Database. Available at MaizeGDB are diverse data that support maize research including maps, gene product information, loci and their various alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis), stocks, sequences, molecular markers, references and contact information for maize researchers worldwide. Also available through MaizeGDB are various community support service bulletin boards including the Editorial Board's list of high-impact papers, information about the Annual Maize Genetics Conference and the Jobs board where employment opportunities are posted. Reported here are data updates, improvements to interfaces and changes to standard operating procedures that have been made during the past 2 years. MaizeGDB is freely available and can be accessed online at http://www.maizegdb.org.

Integrating genetic linkage maps with pachytene chromosome structure in maize.

Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1). all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2). each RN corresponds to one crossover, and (3). the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r(2) = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.

The pam1 gene is required for meiotic bouquet formation and efficient homologous synapsis in maize (Zea mays L.).

The clustering of telomeres on the nuclear envelope (NE) during meiotic prophase to form the bouquet arrangement of chromosomes may facilitate homologous chromosome synapsis. The pam1 (plural abnormalities of meiosis 1) gene is the first maize gene that appears to be required for telomere clustering, and homologous synapsis is impaired in pam1. Telomere clustering on the NE is arrested or delayed at an intermediate stage in pam1. Telomeres associate with the NE during the leptotene-zygotene transition but cluster slowly if at all as meiosis proceeds. Intermediate stages in telomere clustering including miniclusters are observed in pam1 but not in wild-type meiocytes. The tight bouquet normally seen at zygotene is a rare event. In contrast, the polarization of centromeres vs. telomeres in the nucleus at the leptotene-zygotene transition is the same in mutant and wild-type cells. Defects in homologous chromosome synapsis include incomplete synapsis, nonhomologous synapsis, and unresolved interlocks. However, the number of RAD51 foci on chromosomes in pam1 is similar to that of wild type. We suggest that the defects in homologous synapsis and the retardation of prophase I arise from the irregularity of telomere clustering and propose that pam1 is involved in the control of bouquet formation and downstream meiotic prophase I events.